+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12183 | |||||||||||||||
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Title | Salmonella LP ring 26 mer refined in C26 map | |||||||||||||||
Map data | refinement map | |||||||||||||||
Sample |
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Keywords | bacterial flagellum LP ring salmonella / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity Similarity search - Function | |||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi (bacteria) / Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||||||||
Authors | Johnson S / Furlong E | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Nat Microbiol / Year: 2021 Title: Molecular structure of the intact bacterial flagellar basal body. Authors: Steven Johnson / Emily J Furlong / Justin C Deme / Ashley L Nord / Joseph J E Caesar / Fabienne F V Chevance / Richard M Berry / Kelly T Hughes / Susan M Lea / Abstract: The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the ...The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids. Here, we present structures of the intact Salmonella flagellar basal body, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2-3.7 Å. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12183.map.gz | 241.6 MB | EMDB map data format | |
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Header (meta data) | emd-12183-v30.xml emd-12183.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12183_fsc.xml | 15.2 KB | Display | FSC data file |
Images | emd_12183.png | 77.1 KB | ||
Filedesc metadata | emd-12183.cif.gz | 5.7 KB | ||
Others | emd_12183_additional_1.map.gz emd_12183_half_map_1.map.gz emd_12183_half_map_2.map.gz | 34.2 MB 242.7 MB 242.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12183 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12183 | HTTPS FTP |
-Validation report
Summary document | emd_12183_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_12183_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_12183_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | emd_12183_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12183 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12183 | HTTPS FTP |
-Related structure data
Related structure data | 7bglMC 7bhqC 7binC 7bj2C 7bk0C 7nvgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12183.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | refinement map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: post processed
File | emd_12183_additional_1.map | ||||||||||||
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Annotation | post processed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_12183_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_12183_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Flagellar LP ring
Entire | Name: Flagellar LP ring |
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Components |
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-Supramolecule #1: Flagellar LP ring
Supramolecule | Name: Flagellar LP ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) |
-Macromolecule #1: Flagellar L-ring protein
Macromolecule | Name: Flagellar L-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) |
Molecular weight | Theoretical: 24.726666 KDa |
Sequence | String: MQKYALHAYP VMALMVATLT GCAWIPAKPL VQGATTAQPI PGPVPVANGS IFQSAQPINY GYQPLFEDRR PRNIGDTLTI VLQENVSAS KSSSANASRD GKTSFGFDTV PRYLQGLFGN SRADMEASGG NSFNGKGGAN ASNTFSGTLT VTVDQVLANG N LHVVGEKQ ...String: MQKYALHAYP VMALMVATLT GCAWIPAKPL VQGATTAQPI PGPVPVANGS IFQSAQPINY GYQPLFEDRR PRNIGDTLTI VLQENVSAS KSSSANASRD GKTSFGFDTV PRYLQGLFGN SRADMEASGG NSFNGKGGAN ASNTFSGTLT VTVDQVLANG N LHVVGEKQ IAINQGTEFI RFSGVVNPRT ISGSNSVPST QVADARIEYV GNGYINEAQN MGWLQRFFLN LSPM UniProtKB: Flagellar L-ring protein |
-Macromolecule #2: Flagellar P-ring protein
Macromolecule | Name: Flagellar P-ring protein / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) |
Molecular weight | Theoretical: 38.194176 KDa |
Sequence | String: MFKALAGIVL ALVATLAHAE RIRDLTSVQG VRENSLIGYG LVVGLDGTGD QTTQTPFTTQ TLNNMLSQLG ITVPTGTNMQ LKNVAAVMV TASYPPFARQ GQTIDVVVSS MGNAKSLRGG TLLMTPLKGV DSQVYALAQG NILVGGAGAS AGGSSVQVNQ L NGGRITNG ...String: MFKALAGIVL ALVATLAHAE RIRDLTSVQG VRENSLIGYG LVVGLDGTGD QTTQTPFTTQ TLNNMLSQLG ITVPTGTNMQ LKNVAAVMV TASYPPFARQ GQTIDVVVSS MGNAKSLRGG TLLMTPLKGV DSQVYALAQG NILVGGAGAS AGGSSVQVNQ L NGGRITNG AIIERELPTQ FGAGNTINLQ LNDEDFTMAQ QITDAINRAR GYGSATALDA RTVQVRVPSG NSSQVRFLAD IQ NMEVNVT PQDAKVVINS RTGSVVMNRE VTLDSCAVAQ GNLSVTVNRQ LNVNQPNTPF GGGQTVVTPQ TQIDLRQSGG SLQ SVRSSA NLNSVVRALN ALGATPMDLM SILQSMQSAG CLRAKLEII UniProtKB: Flagellar P-ring protein |
-Macromolecule #3: YecR
Macromolecule | Name: YecR / type: protein_or_peptide / ID: 3 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) |
Molecular weight | Theoretical: 12.194968 KDa |
Sequence | String: MKSLIFTLSL LALTGCTITR QAQVSEASPI SGIVRLTYNQ PLFFTSRTDD YVSHGTATRE CQQMGYADAV SFGQPVGTCS IYAGSLCLN TRFTLSWQCR GVAVPQIMPL YY UniProtKB: Uncharacterized protein |
-Macromolecule #4: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4,5-...
Macromolecule | Name: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4,5-bis(oxidanyl)oxane-2-carboxylic acid type: ligand / ID: 4 / Number of copies: 26 / Formula: TLW |
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Molecular weight | Theoretical: 222.193 Da |
Chemical component information | ChemComp-TLW: |
-Macromolecule #5: [(3~{R})-1-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-[[(2~{R},3~{R},4~{...
Macromolecule | Name: [(3~{R})-1-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-(hydroxymethyl)-5-phosphonooxy-4-[(3~{R})-3- ...Name: [(3~{R})-1-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-(hydroxymethyl)-5-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]oxymethyl]-5-oxidanyl-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-2-phosphonooxy-oxan-3-yl]amino]-1-oxidanylidene-tetradecan-3-yl] hexadecanoate type: ligand / ID: 5 / Number of copies: 26 / Formula: TQN |
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Molecular weight | Theoretical: 2.036774 KDa |
Chemical component information | ChemComp-TQN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |